…If you’ve got a burning question or two about the Expelled controversies. Darwin-to-Hitler, doesn’t Sternberg still have his Smithsonian position, the Pepperdine students were extras, the cell animation is plagiarized, Dawkins and P.Z. Myers and all the rest were tricked into granting interviews, Darwin’s Descent of Man was quote-mined, why didn’t Ben Stein just use Google Maps to find the Discovery Institute, ID is religious ’cause Expelled admits it, Yoko Ono is suing…whatevah.

I figured I had to go, if for no other reason than to document what they said, particularly as it related to the movie Expelled and its claims of supposed discrimination against ID proponents like Richard Sternberg. The discussion began on something of a sour note unfortunately (from my POV anyway) as the first thing they did was to request that no one make any private recordings of the session. This was a problem for me since I routinely record such events whenever I attend them.

Now I suppose there could be legitimate reasons for not allowing people to record certain events (like rock concerts etc.) since the material could be bootlegged and sold without permission of the artist. But this wasn’t exactly some big event that they were likely to make a DVD of to sell. It was an informal Q & A with only a handful of people in attendance and only a few of them actively participated in the discussion. Given this, the fact that I have grown more than a bit cynical about how antievolutionists operate, and some of my history with Paul Nelson, I suspect, but cannot prove, that their ban on private recordings was more of a defensive maneuver aimed primarily at me and my companions.

During the debate, which I recorded, Paul relayed an exchange he had via e-mail with paleontologist (and Christian) Keith Miller on the subject of natural vs. intelligent causation. The position he claimed that Miller had taken during this discussion struck me as rather unlikely so I contacted Miller and asked him if Nelson’s characterization of his position was accurate.

Miller responded saying that he not only did not hold the views that Nelson had claimed for him, but that the e-mail exchange that Nelson had quoted from (before an audience of a thousand or more people) had been private and not intended for public consumption.

Since I didn’t have a blog at the time I handed the material over to my friend Ed Brayton who published an account of what happened over on his popular ScienceBlog, Dispatches from the Culture Wars. This led to several follow-up posts with Nelson even leaving a few comments attempting to defend his actions.

So my immediate suspicion was that this history might have led to the “no private recordings” business but then again I could be having delusions of grandeur and it had nothing to do with me or my friends being there with recording devices.

As for the Q & A session that followed it wasn’t what I had hoped in that the subject of the supposedly expelled people in Expelled barely came up. Much of the discussion was on ID creationism in general and a lot of that was a red herring diversion into questions about morality and where it supposedly comes from.

What Paul and his compadres do is conflate evolutionary biology with philosophical materialism (atheism), call it “Darwinism” and then argue that since “Darwinism” does not provide moral absolutes this means that believing in “Darwinism” leads to The Inquisition, witch hunts, anti-Semitic pogroms…oh wait, I mean free sex, marijuana smoking, death metal and The Holocaust.

The point is, evolutionary biology is not atheism, it doesn’t provide moral teachings of any kind and isn’t intended to (no scientific theory does or is). And none of this has anything to do with how accurate and productive evolution is as a scientific theory. It is all beside the point but such questions dominate the thinking of many in the antievolutionist camp.

After the talk Paul came over to me and said that he had noticed that I had been shaking my head rather vigorously during the discussion and he asked me what it was I objected to. I told him he was going to have to be more specific as I was shaking my head a lot (not uncommon for me at creationist events). This particular head shaking was prompted by his response to a question about Michael Behe, common descent, humans, chimps and guinea pigs.

You see the faithful in the pews don’t like it when they hear contradictory things from their leaders in the professional antievolutionist ranks. For example I attended a lecture put on by young Earth creationist (YEC) Walt Brown who caused a lot of agitation in the audience by pooh-poohing the idea of a pre-Noah’s Flood vapor canopy surrounding the Earth (a supposed source for much of the Floodwater). The reason this caused so much consternation was because the vapor canopy (ad hoc) hypothesis has been a staple in YEC teachings for decades and was promoted by the late Henry Morris and his Institute for Creation Research who many YEC look to as the source of all “true” scientific knowledge. Hearing another “creation scientist” being dismissive of a main tenant of ICR style YEC caused a bit of cognitive dissonance and hence squirming in the seats.

In this case the fact that leading ID creationism proponent Michael Behe has on several occasions stated that he believes in common descent (though not mainstream mechanisms behind it) including the idea that humans and chimpanzees share a common ancestor was the source of tension, as Paul Nelson (who is a YEC) and many others in the ID crowd, disagree with Behe on this.

The problem is the idea that humans share a common ancestor with other primates is perhaps the number one thing that creationists don’t want to accept about evolution since, in their eyes, this would deny humans their special place in the universe etc. etc.

During the Biola discussion a woman a few rows ahead of where we were sitting said she had read in one of Behe’s books about how chimpanzees and humans both have the same malfunctioning gene (a pseudogene), which prevents their bodies from being able to synthesis vitamin C (something most other mammals can do) and how Behe thought that this was good evidence for common descent. She said that this “confused” her because it didn’t make sense considering “everything else” (whatever that is). My perception of this was that she wanted reassurances that despite Behe’s place in the pantheon of ID proponents, his views on humans and chimps sharing a common ancestor weren’t true.

Paul answered her by noting that some in ID creationist camp, like Behe, accept common descent but believe (as Behe apparently does) that God controlled this process in some way. He then talked about how it had been discovered that guinea pigs have a similarly malfunctioning gene for vitamin C synthesis and about how many of the mutations in the gene are the same as those found in humans and chimps. He then seemed to imply that if this mutation could be a genetic coincidence then perhaps this and the many other similarities between the human and chimps were just a coincidence as well.

That is what got my head shaking in this case.

First I wanted to see the material on guinea pig genes for myself (never take an antievolutionists word on anything) and I’m currently waiting on a copy of paper on this. I want to see just how similar the guinea pig pseudogene is to ours and then compare this similarity to that which exists between humans and chimps.

Second and much more importantly this particular pseudogene is hardly the only similarity between humans and chimps. There are a whole host of genetic, physiological, anatomical and even behavioral similarities between humans and chimps. So casting aspersions about this single similarity is like bailing water out of the Titanic with a teaspoon and the implication that all these other similarities might be coincidental in a similar fashion really strains credulity.

For example here is another bit of genetic evidence supporting the common ancestry of humans and chimps from Ken Miller (not to be confused with Keith Miller mentioned earlier):

I told Paul that this (the second part) was why I had a problem with his comments. He denied that his telling the woman about guinea pig’s and their pseudogenes was intended to cast doubt on other similarities between humans and chimps, but when my friend Don agreed with my perception of what Paul had said he rather quickly changed the subject to something called ‘orphan genes’ in microorganisms.

From there it devolved into a random discussion, mostly between Don and Paul about the history and philosophy of science as it pertains to evolution.

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27 thoughts on “Expelled Q & A at Biola University”

Don’t hold your breath on the guinea pig pseudo gene. I’ve skimmed two JBC articles on the topic after reading your post (thumbs up, btw!). Apparently the ‘similarity’ of the two pseudogenes stops at ‘both do no longer code for a working protein.’
Taking the functional Rat gene as a model it appears that guinea pigs and primates have lost different exons and managed to include a different number of extra stop codons in what remains of the L-Gulono-y-lactone-Oxidase gene.

Greetings Troy, I have been carrying on my own battle against these ID idiots for over a year in cyberspace. There would be plenty of interesting and lively discussion for you to absorb at http://www.physorg.com It is mainly a science site with a large following and with constantly breaking new developments in all fields of science. If you go to the “Forum” on the right edge and then proceed to the “Creation / Evolution” topic near the bottom, you can find countless threads on varying topics, including the “Expelled” movie. I blog under “photojack” and you can click on any person posting and bring up their posting history, feedback and more. You would be a very welcomed asset to this forum and I personally want to invite you and any scientific friends to join. There are some amazingly inane “religious folks” posting there, so for idle entertainment and wonderment about how these uninformed souls can function in modern society, beware! Be on the lookout for “deadbeat” (appropriate moniker), “newguy”, “pnelson419”, “MisterBelfry” and several other nut cases. On the side of science are myself, “PuckSR”, “gmilam”, “uaafanblog”, “BigDumbWeirdo” (inappropriate moniker), El_Machinae” and others. You would be particularly welcome and could come away with much fodder for the further enlightenment of society in your other realms. Take care, Jack

They write that “when the human and guinea pig sequences (647 nucleotides in total) of the regions of exons 4, 7, 9, 10, and 12 were compared, we found 129 and 96 substitutions in humans and guinea pigs, respectively, when compared with the rat sequences (Fig. 2). The same substitutions from rats to both humans and guinea pigs occurred at 47 nucleotide positions among thr 129 positions where substitutions occurred in the human sequences. A high percentage of the same substitutions in the total substitutions (36%) indicates that there were many hot spots for nucleotide substitutions throughout the sequences examined.” (p. 316)

Lately Royal Truman has given me some pause to doubt this reading of the evidence, but that’s another story. This Nishikimi 2003 paper exists only in hard-copy form (the journal in question doesn’t begin pdfs until 2004), but I’d be happy to mail you a copy if you want it.

“Despite studies focusing on particular bacterial lineages [14], the origin and functions of ORFans remain a mystery [6,15,16]: If proteins in different organisms have descended from common ancestral proteins by duplication and adaptive variation, why is it that so many today show no similarity to each other [4,15]? Why is it that we do not find today any of the necessary ‘intermediate sequences’ that must have given rise to these ORFans?”

Obviously, they need to read more Panda’s Thumb entries ;-) — the ORFans mystery was solved by Ian Musgrave and others a few years ago. Last summer, in the face of the millions of novel sequences his ocean water DNA sampling project turned up, Craig Venter said he no longer accepted the notion of a LUCA. There must have been “thousands” of common ancestors, he said, and they weren’t necessarilyu “so common,” he added (google John Brockman, Life: What A Concept, for the discussion).

More re ORFans — the puzzle appears to extend well beyond prokaryotes and viruses (where thus far it has received the most attention). Check out the fraction of unique sequences in the just-published Tribolium genome:

“The evolutionary emergence of many predicted Tribolium genes is not clear. Thousands of genes currently appear to be species-specific as either no sequence similarity to other genes is detectable, or homology but not orthology can be determined. Reassuringly, this fraction is similar in Tribolium and Drosophila.”

(Nature, a couple of weeks ago)

Heck even lowly H. sapiens appears to have ~1,200 ORFans in our not very sizable genome (1/20 of 24,000, the current total protein-coding sequences estimate for Homo). Eric Lander and colleagues say however that these can’t possibly be real genes, because so many novel sequences could not have emerged since the split with Pan. See their PNAS paper — sorry don’t have the cite handy.

I’m suprised Troy that you didn’t mention our chatting about this with Don and Jim (the Lander paper on human ORFans), because we spent a fair amount of time talking about it, as I indicated that the ORFans phenomenon was not restricted to micro-organisms. My main concern, however (as you recall), was that Lander et al. didn’t assay for possible function any of the sequences they wanted to dump from the human genome as artifacts. Their analysis rested entirely on common ancestry assumptions. Not good.

“The set of orphans thus shows no evidence whatsoever of reading-frame conservation even in our closest primate relatives. (It is of course possible that the orphans include a few valid protein-coding genes, but the proportion must be small enough that it has no discernable effect on the overall RFC distribution.) We conclude that the vast majority of orphans do not correspond to functional protein-coding genes in macaque and chimpanzee, and thus are neither ancestral nor newly arising genes.

If the orphans represent valid human protein-coding genes, we would have to conclude that the vast majority of the orphans were born after the divergence from chimpanzee. Such a model would require a prodigious rate of gene birth in mammalian lineages and a ferocious rate of gene death erasing the huge number of genes born before the divergence from chimpanzee. We reject such a model as wholly implausible. We thus conclude that the vast majority of orphans are simply randomly occurring ORFs that do not represent protein-coding genes.”

What Paul and his compadres do is conflate evolutionary biology with philosophical materialism (atheism) call it “Darwinism” and then argue that since “Darwinism” does not provide moral absolutes. This of course means that believing in “Darwinism” leads to The Inquisition, witch hunts, anti-Semitic pogroms…oh wait, I mean free sex, marijuana smoking, death metal and The Holocaust.

The notion that absolute morality can come from a god has been in theoretical trouble for at least 2400 years, since Plato published his dialogue Euthyphro. Perhaps Nelson and other Creationists are just a little behind on their reading. In practice, Christians are faced with the unavoidable fact that morality has not been absolute, and that the Bible approved of slavery, polygamy, genocide and other practices which are not considered moral by Christians today.

They write that “when the human and guinea pig sequences (647 nucleotides in total) of the regions of exons 4, 7, 9, 10, and 12 were compared, we found 129 and 96 substitutions in humans and guinea pigs, respectively, when compared with the rat sequences (Fig. 2). The same substitutions from rats to both humans and guinea pigs occurred at 47 nucleotide positions among thr 129 positions where substitutions occurred in the human sequences. A high percentage of the same substitutions in the total substitutions (36%) indicates that there were many hot spots for nucleotide substitutions throughout the sequences examined.” (p. 316)

Paul, you’re seriously going to argue that having 36% of substitutions identical in the human & guinea pig pseudogenes, instead of, say 25% (very very approximately what you would expect by chance, but GC content etc. would have a major influence) means that the human pseudogene is not evidence of common ancestry with primate relatives with the pseudogene? I predict that the human pseudogene will be closer in sequence similarity (where alignable, i.e. not deleted or so mutated as to be randomized) to the homologous primate gene than to the guinea pig gene. That’s a prediction based on common ancestry. What’s your prediction based on your creationist speculation?

Re: ORFANs — when it turns out that virtually all of those ORFs in the human genome are artifacts will you then bow to reality and accept common ancestry? They’re not just assuming common ancestry and ignoring the possibility that these things are functional. There are very simple statistical reasons to think they are most not real genes:

“Putative protein-coding genes are identified based on computational analysis of genomic data—typically, by the presence of an open-reading frame (ORF) exceeding {approx}300 bp in a cDNA sequence. The underlying premise, however, is shaky. Recent studies have made clear that the human genome encodes an abundance of non-protein-coding transcripts (1–3). Simply by chance, noncoding transcripts may contain long ORFs. This is particularly so because noncoding transcripts are often GC-rich, whereas stop codons are AT-rich. Indeed, a random GC-rich sequence (50% GC) of 2 kb has a {approx}50% chance of harboring an ORF {approx}400 bases long.”

But no, you think they are evidence that God specially created a bunch of new genes in humans, free from common ancestry & therefore disproving evolution. But random sequences produce lots of ORFs. Follow the evidence wherever it leads, Paul…

They write that “when the human and guinea pig sequences (647 nucleotides in total) of the regions of exons 4, 7, 9, 10, and 12 were compared, we found 129 and 96 substitutions in humans and guinea pigs, respectively, when compared with the rat sequences (Fig. 2). [snip] A high percentage of the same substitutions in the total substitutions (36%) indicates that there were many hot spots for nucleotide substitutions throughout the sequences examined.” (p. 316)

Unfortunately, by using Rat as their comparator in that paper, they have come to a spurious conclusion. Rodents are rapidly evolving, and the apparent “convergence” is actually evolution of the rat sequence. If you compare Guinea pig and primate GLUO sequences to other species, you find that the “convergences” are in fact the ancestral state. Nishikimi et al are wrong, Guniea Pig and Primate sequences are not more convergent than one would expect by chance. (aligned sequences on request).

Nelson: I’m suprised Troy that you didn’t mention our chatting about this with Don and Jim (the Lander paper on human ORFans), because we spent a fair amount of time talking about it, as I indicated that the ORFans phenomenon was not restricted to micro-organisms.

Not surprising to me because it didn’t really stand out that much in my memory of the conversation, at least not in comparison to other things. If only I had a recording I could refer to to… ;)

I’ll add it to the pile of things to look into. Unlike some of you academic types I work for a living.

As shown in figure 4, as the number of viral genomes sequenced increases, the percentage of ORFans drops as relatives are found (just like prokaryotic ORFans). The phage groups with the most “ORFans” are those that have the fewest sequences (just like prokaryotes, which suggests that sampling of genomes is the main issue).

Furthermore, 18% of alleged “ORFans” turn out to be horizontally transferred prokaryotic genes (just as a fair proportion of prokaryotic “ORFans” turn out to be horizontally transferred bacteriophage genes. Looking at the authors conclusions we find them saying:

Because the current sampling of phages (and of bacterial genomes in general), is limited and biased towards particular groups, the percentage of ORFans in different phage groups varies significantly. This low sampling may be a factor contributing to the abundance of phage ORFans, but is not likely to be the only one. That is, even after many more genomes are sequenced, we expect to find a significant number of ORFans and near-ORFans, awaiting interpretation. There are also other possibilities to account for the ORFans’ origin, like rapid divergence after horizontal transfer (from hosts or from other viruses, from existent genomes or yet extinct genomes) or duplication.

Rapid divergence obscuring ancestry in rapidly evolving viruses is by no means unusual, and more careful sequence comparison will undoubtedly turn up more relatives (just as happened with procaryotes).

So, the solutions to the ORFan “puzzle”, as outlined by these authors (poor sampling, horizontal transfer, rapid evolution) follow the same lines as my PT posts (I also included annotation errors, known to produce a proportion of alleged prokaryotic “ORFans”. These annotation errors are likely to be substantial in small genomes as well).

Now that Paul Nelson is aware of this (and he can consult Nishikimi himself to verify), he will have the choice of demonstrating that he is capable of correcting his errors and learning from mistakes, or he can follow what seems to be the modus operandi of the Discovery Institute, and turn the mistake into a lie.

That could actually be the DI’s motto: turning mistakes into lies since 1996 (that’s actually giving them the benefit of the doubt, and assuming that this is only the MO of the Center for Science and Culture).

Reading about this kind of interaction makes me reel. I’d played with the thought of attempting to simply describe the super-simple basics of genetics and natural selection to friends, fellow bloggers, and family. Just to be a source of some rationality.

But just getting a rough idea the endless random and fake flotsam that is thrown in the air to utterly confuse everyone – makes me so discouraged that some joker won’t just come in pull out one sentence from a random real article (or make a fake claim from a non-existent source) and go “ha-HA! I’ve disproved everything!”.

On the one hand, in a blog setting, one can go and do some literature searching, get to the bottom of the bs, and put up a nice point-by-point rebuttal. But, on the other hand, when this nonsense is pulled in person – I mean who knows what random crap their going to pull out of their rears.

Is it even possible to prepare oneself for every new warping of actual observations – which could be pulled from anywhere and any time period – or lying about observations that were never even made?

Clear as mud asks:
How do you do it without just giving up in complete exasperation?

1) You have to have a brain that can retain enormous amounts of information (to nit-pick the details).
2) You have to have the drive, passion and the knowledge that 1 out of 100 people (hopefully) who read blogs like this one will actually use their brain instead of letting other people think for them.
3) You must have a wife or partner who for years has been used (abused?) as a sounding board for your thoughts, ideas and complaints that she hears over and over again on the same subject(s). And yet, this same wife encourages him to go after the brainless bastards.
How silly am I?
I am very proud of Troy and his blog.

Heh. OK, good advice. The third is a trick for most folks, I imagine, so Troy is definitely lucky on that score! The second one is probably the most important. Just keep at it, know that some people will simply never respond, and assume there’s others, however few, who will leave with more knowledge then that with which they arrived.